Sox6 is a multi-faceted transcription factor that has been implicated in regulating differentiation in many development areas, including chondrogenesis, skeletal muscle differentiation, oligodendrocyte and neuronal differentiation, and erythropoiesis, in the mammalian embryo. In some cases, Sox6 seems to act redundantly with the closely-related Sox5 protein, while in others it plays functionally distinct roles. The aim of this project is to survey the role of zebrafish sox6 mutation on the other cell types known to require its function in mammals. Mutant alleles of the sox6 gene in zebrafish Danio rerio have been generated using Zinc finger nuclease (ZFN) targeted mutagenesis. In situ hybridization results revealed a requirement for Sox6, together with Sox5, in oligodendrocyte specification. Combined loss of these two SoxD proteins indicated possible precocious specification of oligodendrocyte progenitor cells (OPCs) at the expense of multipotent progenitor cells (MPCs). sox6 and sox5 were also found to be jointly required for the formation of cartilage and bone. Removal of both gene functions lead to the deformation of pharyngeal arches at 5 dpf, and death before 11 dpf. These results establish a conserved role of sox6 in chondrogenesis and oligodendrogenesis between zebrafish and mice.